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. 2008 Sep 17;130(37):12244-5.
doi: 10.1021/ja804541s. Epub 2008 Aug 19.

Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA

Costin M Gherghe  1 , Zahra Shajani, Kevin A Wilkinson, Gabriele Varani, Kevin M Weeks
Affiliations

Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA

Costin M Gherghe et al. J Am Chem Soc. .

Abstract

The functions of most RNA molecules are critically dependent on the distinct local dynamics that characterize secondary structure and tertiary interactions and on structural changes that occur upon binding by proteins and small molecule ligands. Measurements of RNA dynamics at nucleotide resolution set the foundation for understanding the roles of individual residues in folding, catalysis, and ligand recognition. In favorable cases, local order in small RNAs can be quantitatively analyzed by NMR in terms of a generalized order parameter, S2. Alternatively, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry measures local nucleotide flexibility in RNAs of any size using structure-sensitive reagents that acylate the 2'-hydroxyl position. In this work, we compare per-residue RNA dynamics, analyzed by both S2 and SHAPE, for three RNAs: the HIV-1 TAR element, the U1A protein binding site, and the Tetrahymena telomerase stem loop 4. We find a very strong correlation between the two measurements: nucleotides with high SHAPE reactivities consistently have low S2 values. We conclude that SHAPE chemistry quantitatively reports local nucleotide dynamics and can be used with confidence to analyze dynamics in large RNAs, RNA-protein complexes, and RNAs in vivo.

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Figures

Figure 1
Figure 1
Schemes for interpreting (A) the generalized order parameter S2, and (B) RNA SHAPE chemistry.
Figure 2
Figure 2
Local nucleotide structure in RNA analyzed by SHAPE and S2. (A) Secondary structures for the TAR, U1A target, and T-SL4 RNAs. Nucleotides with SHAPE reactivities greater than 0.5 for TAR and U1A, or greater than 0.6 for T-SL4 are red. Positions for which S2 was not obtained are shown as red or black spheres. (B). Histograms of SHAPE reactivities as a function of nucleotide position (columns) compared to 1-S2 measurements (blue spheres).
Figure 3
Figure 3
Quantitative correlation between SHAPE reactivity and (A) S2, measured at C1', or (B) solvent accessibility of the 2'-hydroxyl group. Pearson's linear R-values are shown.
See this image and copyright information in PMC

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